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Structure of tetrahydrodipicolinate N-succinyltransferase (RV1201C; dapd) from mycobacterium tuberculosis
Analyse Structure of tetrahydrodipicolinate N-succinyltransferase (RV1201C; dapd) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FSX
- Type
- protein
- Length
- 1,503 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tetrahydrodipicolinate N-succinyltransferase
- EC
- 2.3.1.117
- UniProt
- O05302
- Ligands
- MG, NA
- Pockets
- 10 · best druggability 0.80
Structure
x-ray diffraction · 5 distinct chains · 14% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tetrahydrodipicolinate N-succinyltransferase (EC 2.3.1.117) | protein | 300 | 15% helix, 35% strand | O05302 |
| B | Tetrahydrodipicolinate N-succinyltransferase (EC 2.3.1.117) | protein | 306 | 13% helix, 33% strand | O05302 |
| C | Tetrahydrodipicolinate N-succinyltransferase (EC 2.3.1.117) | protein | 300 | 14% helix, 33% strand | O05302 |
| D | Tetrahydrodipicolinate N-succinyltransferase (EC 2.3.1.117) | protein | 307 | 13% helix, 33% strand | O05302 |
| E | Tetrahydrodipicolinate N-succinyltransferase (EC 2.3.1.117) | protein | 290 | 14% helix, 35% strand | O05302 |
Ligands and binding sites
- MG · Magnesium ion · metal · 9 copies · chains A, B, C, D, E
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D, E
- ACY · Acetic acid · additive · 4 copies · chains A, C, B, D
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 3 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 628 | 0.80 | 0.85 | 95 | MG |
| 2 | 770 | 0.73 | 0.78 | 110 | ACY |
| 3 | 216 | 0.69 | 0.86 | 43 | empty |
| 4 | 602 | 0.68 | 0.77 | 54 | ACY |
| 5 | 178 | 0.54 | 0.79 | 25 | ACY |
Interfaces
6 interfaces between chains.
- A–B · 1742 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 1738 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 1591 Ų buried · 25 hydrogen bonds · protein-protein
- A–D · 406 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 234 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3FSX · Structure of tetrahydrodipicolinate N-succinyltransferase (Rv1201c; DapD) from… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt O05302
- Elsewhere: RCSB PDB 3FSX · PDBe 3FSX · UniProt O05302
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